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Advancements in microscopy instrumentation have resulted in larger volumes of acquired image data and, consequently, increased memory and space requirements for the processing and storage of the data. To address the issue in software, the Microscopy Image Analysis Tool (MIATool) was created to support processing of large image sets that makes efficient use of available resources. Implemented in MATLAB using object-oriented design, MIATool works with image pointer arrays to utilize RAM effectively and to support the analysis of different interpretations of data. Furthermore, the software provides image editing tools which operate on parameter objects that are saved in lieu of processed images to exploit the available disk space. A detailed image analysis example is given to illustrate the design and features of MIATool.